This is the golden question of the century. It appears MSE does not play fair with other AVs when upgrading.
I am using Threatfire on the side and MSE's upgrade kept giving me errors. After trying variations with my install process, disabling TF (not uninstalling) I came to the realization that it is not playing when it says you have to uninstall your other AV.
So download the MSE installer from the website (I avoid MSE upgrades/updates through Windows update), I also downloaded a new installer for my other AV (just in case there is a newer build for that as well)
I disconnected my internet, uninstalled both AVs - made sure all was removed through the add/remove/registry/windows install cleaner and installed MSE then TF and it appears to be ok so far -
2 Things I have learned:
1) Install with a fresh installer - don't run the upgrade/windows update options
2) Make sure all other AVs are uninstalled
I can't guarantee this is a consistent process for all machines, but it has finally worked for me
goodluck
